Despite being the world’s largest batoid fish, manta rays have been the focus of very little research in the last century. Almost nothing is currently known about their ecology or distribution throughout the world’s oceans. Manta rays are considered to be near-threatened to vulnerable by the World Conservation Union’s Redlist of endangered species, yet many populations still face threats from target fishing for their fin cartilage, branchial filaments and meat. The taxonomic history of the genus Manta has been questionable and convoluted,with Manta having one of the most extensive generic and species synonymies of any living genus of cartilaginous fish. Currently this genus is considered to be monotypicwith a single recognized species, Manta birostris. Behavioural and morphological data collected during this study showed that there are two distinct, sympatric species of manta ray in Mozambique. This discovery has led to an examination of manta ray distribution worldwide, with the two species hypothesis receiving further support from study sites in the Indian and Pacific Oceans. This thesis examined large populations of both putative species in Mozambique. Development and application of a photographic-identification methodology allowed identification of individuals based on their unique ventral surface markings (spots). The ability to recognise individuals enabled many aspects of both populations to be examined. A total of 449 individual rays were identified of Manta birostris variant A and 101 individual rays were identified of Manta birostris variant B. Both populations exhibited a highly significant female bias in observed sex ratios of 1:3.5 and 1:7.4 respectively. The photographic identification approach was used in studies of population size and structure and to examine the reproductive ecology of these two distinct populations. Population estimates incorporating four years of re-sighting data on Manta birostris variant A and five years of data on Manta birostris variant B were conducted using the program MARK resulting in super population estimates of 890 and 600 individuals respectively. The region encompassing the study site was identified as a mating ground for Manta birostris variant A based on observations of mating events and fresh pectoral fin tip scars on female rays produced when the male rays bite onto the fins during copulation. The distribution of scars was highly biased, with 99% on the left pectoral fin, indicative of a strong lateralised behavioural trait in this species. No other elasmobranch has been reported to display behavioural lateralisation. The study region also acts as a birthing ground, with individuals giving birth in the summer after a gestation period of approximately one year. Reproductive periodicity in M. birostris variant A was most commonly biennial, but a few individuals were seen to be pregnant in consecutive years, confirming an annual ovulatory cycle. The production of a single pup appears to be the normal situation, although observations in the wild as well as during opportunistic dissections of individuals killed in fisheries revealed that two pups are conceived on occasion. Morphometric analysis of late-term foetus (M. birostris variant A) was contrasted with measurements taken from adult rays. These are the only detailed measurements on M. birostris variant A from the western Indian Ocean. Predatory scarring and bite injuries on individuals of both variant A and B were consistent with attacks from sharks of various sizes. The frequency and effect of these predatory injuries on the two populations were examined over a three-year period. Acoustic tags were attached to fourteen rays and their presence/absence at sites around the major inshore reefs was explored to evaluate how the rays utilised their environment on a temporal scale. Cleaning activity of both putative species of manta rays by small fishes occurred on these reefs and was considered to be the main reason why the rays were present at these sites. Parasite removal and wound healing were implicated as the benefits received. Host cleaner fish species partition the manta ray body to avoid interspecific competition while the two putative species appear to partition cleaning habitats, with very little overlap apparent. This research on manta rays is the first of its kind in African waters. Many aspects of the study have contributed to the limited baseline data currently available for this genus. The study additionally provided sufficient empirical evidence to warrant the separation of these two putative species of Manta and a full revision of the genus with the systematic examination of specimens throughout Manta’s range. The results of this study may be useful in this endeavour as diagnostic characteristics have been isolated that may help to differentiate members of this genus. The results of this research study are directly applicable to management strategies for both putative species of manta rays off the East Coast of Africa as well as populations worldwide and have highlighted the potential need for different conservation strategies

Despite being the world’s largest batoid fish, manta rays have been the focus of very little research in the last century. Almost nothing is currently known about their ecology or distribution throughout the world’s oceans. Manta rays are considered to be near-threatened to vulnerable by the World Conservation Union’s Redlist of endangered species, yet many populations still face threats from target fishing for their fin cartilage, branchial filaments and meat. The taxonomic history of the genus Manta has been questionable and convoluted,with Manta having one of the most extensive generic and species synonymies of any living genus of cartilaginous fish. Currently this genus is considered to be monotypicwith a single recognized species, Manta birostris. Behavioural and morphological data collected during this study showed that there are two distinct, sympatric species of manta ray in Mozambique. This discovery has led to an examination of manta ray distribution worldwide, with the two species hypothesis receiving further support from study sites in the Indian and Pacific Oceans. This thesis examined large populations of both putative species in Mozambique. Development and application of a photographic-identification methodology allowed identification of individuals based on their unique ventral surface markings (spots). The ability to recognise individuals enabled many aspects of both populations to be examined. A total of 449 individual rays were identified of Manta birostris variant A and 101 individual rays were identified of Manta birostris variant B. Both populations exhibited a highly significant female bias in observed sex ratios of 1:3.5 and 1:7.4 respectively. The photographic identification approach was used in studies of population size and structure and to examine the reproductive ecology of these two distinct populations. Population estimates incorporating four years of re-sighting data on Manta birostris variant A and five years of data on Manta birostris variant B were conducted using the program MARK resulting in super population estimates of 890 and 600 individuals respectively. The region encompassing the study site was identified as a mating ground for Manta birostris variant A based on observations of mating events and fresh pectoral fin tip scars on female rays produced when the male rays bite onto the fins during copulation. The distribution of scars was highly biased, with 99% on the left pectoral fin, indicative of a strong lateralised behavioural trait in this species. No other elasmobranch has been reported to display behavioural lateralisation. The study region also acts as a birthing ground, with individuals giving birth in the summer after a gestation period of approximately one year. Reproductive periodicity in M. birostris variant A was most commonly biennial, but a few individuals were seen to be pregnant in consecutive years, confirming an annual ovulatory cycle. The production of a single pup appears to be the normal situation, although observations in the wild as well as during opportunistic dissections of individuals killed in fisheries revealed that two pups are conceived on occasion. Morphometric analysis of late-term foetus (M. birostris variant A) was contrasted with measurements taken from adult rays. These are the only detailed measurements on M. birostris variant A from the western Indian Ocean. Predatory scarring and bite injuries on individuals of both variant A and B were consistent with attacks from sharks of various sizes. The frequency and effect of these predatory injuries on the two populations were examined over a three-year period. Acoustic tags were attached to fourteen rays and their presence/absence at sites around the major inshore reefs was explored to evaluate how the rays utilised their environment on a temporal scale. Cleaning activity of both putative species of manta rays by small fishes occurred on these reefs and was considered to be the main reason why the rays were present at these sites. Parasite removal and wound healing were implicated as the benefits received. Host cleaner fish species partition the manta ray body to avoid interspecific competition while the two putative species appear to partition cleaning habitats, with very little overlap apparent. This research on manta rays is the first of its kind in African waters. Many aspects of the study have contributed to the limited baseline data currently available for this genus. The study additionally provided sufficient empirical evidence to warrant the separation of these two putative species of Manta and a full revision of the genus with the systematic examination of specimens throughout Manta’s range. The results of this study may be useful in this endeavour as diagnostic characteristics have been isolated that may help to differentiate members of this genus. The results of this research study are directly applicable to management strategies for both putative species of manta rays off the East Coast of Africa as well as populations worldwide and have highlighted the potential need for different conservation strategies

Despite being the world’s largest batoid fish, manta rays have been the focus of very little research in the last century. Almost nothing is currently known about their ecology or distribution throughout the world’s oceans. Manta rays are considered to be near-threatened to vulnerable by the World Conservation Union’s Redlist of endangered species, yet many populations still face threats from target fishing for their fin cartilage, branchial filaments and meat. The taxonomic history of the genus Manta has been questionable and convoluted,with Manta having one of the most extensive generic and species synonymies of any living genus of cartilaginous fish. Currently this genus is considered to be monotypicwith a single recognized species, Manta birostris. Behavioural and morphological data collected during this study showed that there are two distinct, sympatric species of manta ray in Mozambique. This discovery has led to an examination of manta ray distribution worldwide, with the two species hypothesis receiving further support from study sites in the Indian and Pacific Oceans. This thesis examined large populations of both putative species in Mozambique. Development and application of a photographic-identification methodology allowed identification of individuals based on their unique ventral surface markings (spots). The ability to recognise individuals enabled many aspects of both populations to be examined. A total of 449 individual rays were identified of Manta birostris variant A and 101 individual rays were identified of Manta birostris variant B. Both populations exhibited a highly significant female bias in observed sex ratios of 1:3.5 and 1:7.4 respectively. The photographic identification approach was used in studies of population size and structure and to examine the reproductive ecology of these two distinct populations. Population estimates incorporating four years of re-sighting data on Manta birostris variant A and five years of data on Manta birostris variant B were conducted using the program MARK resulting in super population estimates of 890 and 600 individuals respectively. The region encompassing the study site was identified as a mating ground for Manta birostris variant A based on observations of mating events and fresh pectoral fin tip scars on female rays produced when the male rays bite onto the fins during copulation. The distribution of scars was highly biased, with 99% on the left pectoral fin, indicative of a strong lateralised behavioural trait in this species. No other elasmobranch has been reported to display behavioural lateralisation. The study region also acts as a birthing ground, with individuals giving birth in the summer after a gestation period of approximately one year. Reproductive periodicity in M. birostris variant A was most commonly biennial, but a few individuals were seen to be pregnant in consecutive years, confirming an annual ovulatory cycle. The production of a single pup appears to be the normal situation, although observations in the wild as well as during opportunistic dissections of individuals killed in fisheries revealed that two pups are conceived on occasion. Morphometric analysis of late-term foetus (M. birostris variant A) was contrasted with measurements taken from adult rays. These are the only detailed measurements on M. birostris variant A from the western Indian Ocean. Predatory scarring and bite injuries on individuals of both variant A and B were consistent with attacks from sharks of various sizes. The frequency and effect of these predatory injuries on the two populations were examined over a three-year period. Acoustic tags were attached to fourteen rays and their presence/absence at sites around the major inshore reefs was explored to evaluate how the rays utilised their environment on a temporal scale. Cleaning activity of both putative species of manta rays by small fishes occurred on these reefs and was considered to be the main reason why the rays were present at these sites. Parasite removal and wound healing were implicated as the benefits received. Host cleaner fish species partition the manta ray body to avoid interspecific competition while the two putative species appear to partition cleaning habitats, with very little overlap apparent. This research on manta rays is the first of its kind in African waters. Many aspects of the study have contributed to the limited baseline data currently available for this genus. The study additionally provided sufficient empirical evidence to warrant the separation of these two putative species of Manta and a full revision of the genus with the systematic examination of specimens throughout Manta’s range. The results of this study may be useful in this endeavour as diagnostic characteristics have been isolated that may help to differentiate members of this genus. The results of this research study are directly applicable to management strategies for both putative species of manta rays off the East Coast of Africa as well as populations worldwide and have highlighted the potential need for different conservation strategies

Despite being the world’s largest batoid fish, manta rays have been the focus of very little research in the last century. Almost nothing is currently known about their ecology or distribution throughout the world’s oceans. Manta rays are considered to be near-threatened to vulnerable by the World Conservation Union’s Redlist of endangered species, yet many populations still face threats from target fishing for their fin cartilage, branchial filaments and meat. The taxonomic history of the genus Manta has been questionable and convoluted,with Manta having one of the most extensive generic and species synonymies of any living genus of cartilaginous fish. Currently this genus is considered to be monotypicwith a single recognized species, Manta birostris. Behavioural and morphological data collected during this study showed that there are two distinct, sympatric species of manta ray in Mozambique. This discovery has led to an examination of manta ray distribution worldwide, with the two species hypothesis receiving further support from study sites in the Indian and Pacific Oceans. This thesis examined large populations of both putative species in Mozambique. Development and application of a photographic-identification methodology allowed identification of individuals based on their unique ventral surface markings (spots). The ability to recognise individuals enabled many aspects of both populations to be examined. A total of 449 individual rays were identified of Manta birostris variant A and 101 individual rays were identified of Manta birostris variant B. Both populations exhibited a highly significant female bias in observed sex ratios of 1:3.5 and 1:7.4 respectively. The photographic identification approach was used in studies of population size and structure and to examine the reproductive ecology of these two distinct populations. Population estimates incorporating four years of re-sighting data on Manta birostris variant A and five years of data on Manta birostris variant B were conducted using the program MARK resulting in super population estimates of 890 and 600 individuals respectively. The region encompassing the study site was identified as a mating ground for Manta birostris variant A based on observations of mating events and fresh pectoral fin tip scars on female rays produced when the male rays bite onto the fins during copulation. The distribution of scars was highly biased, with 99% on the left pectoral fin, indicative of a strong lateralised behavioural trait in this species. No other elasmobranch has been reported to display behavioural lateralisation. The study region also acts as a birthing ground, with individuals giving birth in the summer after a gestation period of approximately one year. Reproductive periodicity in M. birostris variant A was most commonly biennial, but a few individuals were seen to be pregnant in consecutive years, confirming an annual ovulatory cycle. The production of a single pup appears to be the normal situation, although observations in the wild as well as during opportunistic dissections of individuals killed in fisheries revealed that two pups are conceived on occasion. Morphometric analysis of late-term foetus (M. birostris variant A) was contrasted with measurements taken from adult rays. These are the only detailed measurements on M. birostris variant A from the western Indian Ocean. Predatory scarring and bite injuries on individuals of both variant A and B were consistent with attacks from sharks of various sizes. The frequency and effect of these predatory injuries on the two populations were examined over a three-year period. Acoustic tags were attached to fourteen rays and their presence/absence at sites around the major inshore reefs was explored to evaluate how the rays utilised their environment on a temporal scale. Cleaning activity of both putative species of manta rays by small fishes occurred on these reefs and was considered to be the main reason why the rays were present at these sites. Parasite removal and wound healing were implicated as the benefits received. Host cleaner fish species partition the manta ray body to avoid interspecific competition while the two putative species appear to partition cleaning habitats, with very little overlap apparent. This research on manta rays is the first of its kind in African waters. Many aspects of the study have contributed to the limited baseline data currently available for this genus. The study additionally provided sufficient empirical evidence to warrant the separation of these two putative species of Manta and a full revision of the genus with the systematic examination of specimens throughout Manta’s range. The results of this study may be useful in this endeavour as diagnostic characteristics have been isolated that may help to differentiate members of this genus. The results of this research study are directly applicable to management strategies for both putative species of manta rays off the East Coast of Africa as well as populations worldwide and have highlighted the potential need for different conservation strategies

Despite being the world’s largest batoid fish, manta rays have been the focus of very little research in the last century. Almost nothing is currently known about their ecology or distribution throughout the world’s oceans. Manta rays are considered to be near-threatened to vulnerable by the World Conservation Union’s Redlist of endangered species, yet many populations still face threats from target fishing for their fin cartilage, branchial filaments and meat. The taxonomic history of the genus Manta has been questionable and convoluted,with Manta having one of the most extensive generic and species synonymies of any living genus of cartilaginous fish. Currently this genus is considered to be monotypicwith a single recognized species, Manta birostris. Behavioural and morphological data collected during this study showed that there are two distinct, sympatric species of manta ray in Mozambique. This discovery has led to an examination of manta ray distribution worldwide, with the two species hypothesis receiving further support from study sites in the Indian and Pacific Oceans. This thesis examined large populations of both putative species in Mozambique. Development and application of a photographic-identification methodology allowed identification of individuals based on their unique ventral surface markings (spots). The ability to recognise individuals enabled many aspects of both populations to be examined. A total of 449 individual rays were identified of Manta birostris variant A and 101 individual rays were identified of Manta birostris variant B. Both populations exhibited a highly significant female bias in observed sex ratios of 1:3.5 and 1:7.4 respectively. The photographic identification approach was used in studies of population size and structure and to examine the reproductive ecology of these two distinct populations. Population estimates incorporating four years of re-sighting data on Manta birostris variant A and five years of data on Manta birostris variant B were conducted using the program MARK resulting in super population estimates of 890 and 600 individuals respectively. The region encompassing the study site was identified as a mating ground for Manta birostris variant A based on observations of mating events and fresh pectoral fin tip scars on female rays produced when the male rays bite onto the fins during copulation. The distribution of scars was highly biased, with 99% on the left pectoral fin, indicative of a strong lateralised behavioural trait in this species. No other elasmobranch has been reported to display behavioural lateralisation. The study region also acts as a birthing ground, with individuals giving birth in the summer after a gestation period of approximately one year. Reproductive periodicity in M. birostris variant A was most commonly biennial, but a few individuals were seen to be pregnant in consecutive years, confirming an annual ovulatory cycle. The production of a single pup appears to be the normal situation, although observations in the wild as well as during opportunistic dissections of individuals killed in fisheries revealed that two pups are conceived on occasion. Morphometric analysis of late-term foetus (M. birostris variant A) was contrasted with measurements taken from adult rays. These are the only detailed measurements on M. birostris variant A from the western Indian Ocean. Predatory scarring and bite injuries on individuals of both variant A and B were consistent with attacks from sharks of various sizes. The frequency and effect of these predatory injuries on the two populations were examined over a three-year period. Acoustic tags were attached to fourteen rays and their presence/absence at sites around the major inshore reefs was explored to evaluate how the rays utilised their environment on a temporal scale. Cleaning activity of both putative species of manta rays by small fishes occurred on these reefs and was considered to be the main reason why the rays were present at these sites. Parasite removal and wound healing were implicated as the benefits received. Host cleaner fish species partition the manta ray body to avoid interspecific competition while the two putative species appear to partition cleaning habitats, with very little overlap apparent. This research on manta rays is the first of its kind in African waters. Many aspects of the study have contributed to the limited baseline data currently available for this genus. The study additionally provided sufficient empirical evidence to warrant the separation of these two putative species of Manta and a full revision of the genus with the systematic examination of specimens throughout Manta’s range. The results of this study may be useful in this endeavour as diagnostic characteristics have been isolated that may help to differentiate members of this genus. The results of this research study are directly applicable to management strategies for both putative species of manta rays off the East Coast of Africa as well as populations worldwide and have highlighted the potential need for different conservation strategies

Hermit crabs form an important component of the marine benthos and globally more than 1,200 species have been described. In the unique bioregion of South Africa, hermit crabs are poorly known, and the last taxonomic revision of the group was that of K. H. Barnard in 1950, who recorded only 32 species. This study combines morphological taxonomy, threedimensional (3D) micro-computed tomography (µCT) visualisations, and molecular barcoding to add to, revise, and provide an updated listing of, the regional fauna. The first section of the thesis comprises four chapters, each giving a detailed account of a species either new to science, or to the region. The pagurid hermit crab Goreopagurus poorei, a new species and genus record to the country, is reported and described from deep sea habitats along the Agulhas Shelf, extending the distribution by >10,000 km across the Indian Ocean. Furthermore, three species are described as new to science, one each from the three most common families. The first of these, a deep-water species from a genus of the family Parapaguridae that was previously unknown to South Africa, Paragiopagurus atkinsonae n. sp., is fully described and illustrated, and compared with two other parapagurids that each play a dominant role in the regional benthic offshore invertebrate community. The other two species new to science, Diogenes n. sp. from the family Diogenidae, and Pagurus n. sp. from the family Paguridae, inhabit coastal reefs in subtidal waters off southern KwaZulu-Natal. For the first time in crustacean taxonomy, species descriptions, particularly the one of Pagurus n. sp., are informed by, or based on, µCT imagery of calcified body parts. Following on this technique, Chapter 6 is a short presentation of the 3D raw dataset of seven µCT scans of types and rare museum specimens used in this thesis, which is made publicly available for download. The taxonomic use of the scanning method, with disseminating volumetric data of hermit crabs, is discussed briefly. The final section investigates the fauna as a whole. In Chapter 7, 194 cytochrome c oxidase subunit I gene segments (COI ‘barcodes’) of 43 nominal species plus 12 additional putative species (n = 55 species-like units) were used to validate morphological identifications. Testing this dataset revealed high barcoding efficacy, with nearly 99% identification success rates, and with the best Kimura 2-parameter distance to safely delimit species of hermit crabs of about 3.5%. Chapter 8 updates the regional fauna and provides taxonomic accounts for 62 nominal species which have either been added subsequent to the previous monographic review, or which have undergone taxonomic revision since that time. Of these, 12 are added for the first time here, increasing the number of known South African hermit crab species to 72, an expansion of 56% since Barnard, and about 20% since a recent species list published by W. Emmerson in 2016. Because colour images are provided for 51 out of 72 species, Chapter 8 can also be used as a preliminary guide. However, this study has shown that the hermit crabs of South Africa are by far more diverse than originally thought, and the summary, which includes only the 72 nominal taxa and none of the additional 10 putative species included in the barcoding dataset, is speculated to be only 60–70% complete. Future taxonomic work, especially in the genera Diogenes and Paguristes, will most likely result in many more species descriptions. Therefore, this current study is to be seen as important step towards a fully illustrated taxonomic catalogue on the South African hermit crabs to be produced in the near future.

This thesis investigates the diversity of two silica-scaled protist groups, Paraphysomonadida and Thaumatomonadida by light and electron microscopical observations and sequencing (rDNA) on novel clonal cultures. Despite these groups of protist dominating pelagic, littoral as well as inland freshwater and soil habitats, they are taxonomically poorly understood to the extent that any progress in ecological theory is hampered. Now that environmental DNA sequencing is being carried out faster than we can characterise protists from culture it is important that we understand how molecular and physical diversity match up, especially because so many protists are morphospecies. Nearly one hundred isolates were cultured on which both morphological and molecular data was carried out in parallel to reveal around 50 new species of protist from eight different genera: two heterokont genera, Paraphysomonas and Incisomonas n. gen., and six cercozoan genera, Thaumatomonas, Allas, Reckertia, Thaumatospina n. gen., Cowlomonas n. gen., and Scutellomonas n. gen. These data make major contributions to taxonomy and understanding aspects of protist diversity where previously morphological diversity was heavily biased towards over- generalized morphotypes. This thesis quickly showed that gross lumping of morphospecies was true of Paraphysomonas, for which many of the isolates cultured herein might have been regarded as one species (not more than 20). The many cultured isolates exhibited varied cell and scale morphology, and by sequencing (rDNA), it was possible to see the evolution of scale morphology map on to trees. This marriage of molecular and morphological data made it possible to view distinct groups of species that shared scale detail that might have otherwise been overlooked had either method been used alone. This research has shed significant light on how scale morphology can be used as reliable taxonomic marker for protists, the insights of which can be applied to make taxonomic improvements to other silica-scaled protist groups.